Open cmdcolin opened 1 year ago
also, more "tutorials" like https://github.com/GMOD/jbrowse-components/pull/3449
another doc topic, plugins https://github.com/GMOD/jbrowse-plugin-template/issues/30
may be a good example for jexl docs https://github.com/GMOD/jbrowse-components/discussions/3603#discussioncomment-5470742
just for context, @carolinebridge-oicr and i were talking in chat just about the setup of jbrowse with the overture team, etc. I think the embedded deployment is difficult for a number of reasons
also, it may be worth steering people to our working examples e.g. storybook and embedded_demos over the tutorial page
I know we have the state model reference, but I think for anything embedded view relevant we should have a separate, clearly documented API for things like showTracks. Could link out to the storybooks too.
example for variation track color https://github.com/GMOD/jbrowse/issues/937#issuecomment-1534326753
advanced example of config (setting color, etc) at https://jbrowse.org/jb2/docs/config_guides/quantitative_track/ (recommended by veupathdb)
Update docs with HiDPI screenshots...many are low res
bookmark docs need updating http://jbrowse.org/jb2/docs/user_guides/bookmark_widget/
improve synteny docs https://github.com/GMOD/jbrowse-components/issues/3270
do we have enough discoverability in our documentation for cross-regional visualizations / data rendering? we've got a ton of support for it at this point might be worth having a dedicated page for it in our user guide
yes could be worthwhile, or at least expanding documentation around the features that use this mode
paired bedpe display needs docs
Review quickstart guide: this is an important document, and in the middle it switches from using npx serve to --out /var/www/html/jbrowse2 without explanation
https://jbrowse.org/jb2/docs/quickstart_web/
Also review this repo's README.md. could be made more minimal, as people might find it, thinking they need to apt install things when they dont really
I also still think there is value in making a superquickstart. it could be made into a TLDR at the top of the quickstart. this was, at one point, deleted but i think it helps to orient someone about a cli workflow without a lot of prose. it is hard to scan the document at a high level
the quickstart also does not have links to example files. it could essentially mirror the protocols paper, but with smaller files
possible idea; use an ai to aid documentation process. AI can generate a bunch of plausible looking stuff, lowering the barrier to just getting it done. we have not established guidelines about using AI generated content in our project but if it is acceptable, it might be worth trying out
mention in various places where plugins are documented e.g. https://jbrowse.org/jb2/docs/tutorials/no_build_plugin_tutorial/ that embedded apps can use a different technique
Storybook: document the usage of trackId for text indexing (mentioned by @kuffelgr on chat)done